Upgrade CF9 to CF11 w/IIS can't get to migration/configuration stage

I finally go approval to do my upgrade not as a stand alone, side-by-side upgrade which was requiring me to do a major hack that wasn't working due to our funky coding and security twists we have implemented in the code.
Unfortunately, when I do the upgrade/installation it installs, but I can't move on to the migration/configuration stage of the installation.  I can't see anything in the error logs.  Sometimes I'll get the 500.19 error message when I try to connect to the administrator myself, other times nothing.  When I get the HTTP Error 500.19 Internal Server Error it refers to the ApplicationHost.config or web.config file that contains malformed xml element.  When I look at the old web.config file it contains about 9 handlers that are using either jrun_iis6_wildcard.dll or jrun_iis6.dll.  I do have the IIS6 to IIS7 configuration selected in the new installation of CF11, but I can't move forward.  I want to just copy these 2 files from my CF9 installation, but I don't know where to put them.  I've even renamed the web.config file so that IIS would recreate it so it wouldn't be referring to the old CF9 web.config file and getting stuck there, which one error message once referred to these lines in the CF9 web.config file.  I understand that this question blurs the ColdFusion/IIS category boundaries.  I'm not sure where my error is lying, with IIS or CF11.  I want to just enter these handlers manually in IIS 7, but my boss seems to think we need to have wsconfig do that for us in case it is putting code elsewhere and we are missing configuration changes that really puts us in a spiral.  Thoughts/suggestions anyone?  I hope I was clear enough.
Another thing is that we have our CFIDE folder for CF9 located in a different directory, for security purposes I'm guessing, yet I can't figure out how CF is recognizing that it should go there to run.  In CF Administrator it is referring to a different folder for CFIDE that doesn't exist.  I have only seen one referrence to the correct location, and that was in the registry when I was ensuring CF11 references were deleted. CF9 had it there. I guess I'm wondering if there is a setting somewhere that i need to change so CF11 will look in the correct location and then run and go forward with the migration/configuration part of the instalation.  I can't find it in any of my searches that look for that foldername in the files.
I have inherited this project and there is very little documented regarding configuration changes that were done.
Thanks in advance!!
Jennifer

OK, my installation is working, although I'm still trying to get the applications to work (permissions issues I think).  Since I kept having migration difficulties we created a CAR first with CF9.  We then ended up just doing a straight upgrade on our development server.  I performed the install with server configuration and selected Configure my webserver for ColdFusion 11, IIS.  When you launch the browser to connect to CF11 administrator if you get the 500 error message it may be because the SSL for the CFIDE>Administrator folder in IIS is selected.  Deselect it and that error messge should go away (if it is that that is).  We kept getting a 404.7 error message of deny file extension.  I was thinking it had to do with my cfm extensions because I was trying to open a cfm, but it wasn't the case.  The error message mentioned isapi.redirect.dlls.  I finally found an error message under my IIS FailedRequestLogs that mentioned something about Request Filtering.  Turns out .dll was not in the allowed list of my virtual Jakarta folder.  Once I added this and restarted IIS I was able to get into my CF Administrator 11 and installed the CAR file.
Now I keep getting Unauthorized errors and need to figure that out. Permissions are looking like the cause of that.
Things I learned (you may already know this):
CF9 can have CFIDE placed wherever, but CF11 needs to keep it where it is installed.
CF11 doesn't need IIS 6 Metabase Compatability installed, whereas CF9 did (at least ours did)
We kept getting a duplicat MIME Type error message too for .air.  That was added at the server level and inherited at the website level.  I deleted it at the server level and added it at the website level.
I hope this helps someone.

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